The pollution of water is a major problem in many parts of the world. In many developing countries, aquatic systems are receiving untreated or partially treated effluents, containing anthropogenic pollutants whereas these rivers serve as a basic network for human and animal consumption. High values of toxic metals, persistent organic pollutants (POPs), faecal indicator bacteria (FIBs), antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) in rivers may pose a great risk to human health and aquatic living organisms. The main objective of the research is to assess the prevalence and dissemination of toxic metals, POPs, FIB, ARB and ARGs in the rivers of Kinshasa (Republic Democratic of the Congo) as a study case. Overall, the present work demonstrated that chemical and microbiological pollution can exceed, in many studied sites, the international recommendation for water quality and has the potential to affect ecosystem functions as well as human impact.